Is it a mod that adds the YOUTUBE bbcode? Then you'd have to find out if they can help you. If it is a mod then I'd guess that it uses a hook that isn't called from the admincp.
If I understand things (based on a quick look at the code, so I may not understand), when you set the cache time to 0 the cached posts will get deleted as soon as the Cleanup #2 scheduled task runs, so they may have already have been deleted anyway. But like I said before, if the cache time is > 0 then the cache will get built as users view posts, so that seems like it could even be better than building it all at once from the admincp (unless you were doing it in the middle of the night or something).
Edit: reading your post again, I'm thinking maybe there's a misunderstanding about the problem. I'm thinking if the post cache has been built incorrectly, then you'd have to build it again even if the problem were fixed. It sounds like maybe you're thinking that you could fix the problem and avoid rebuilding the cache? I suppose that's a possibility, depending on how the mod works.
In any case, that's all I have to say, I'll let someone else help.